Well after much testing I solved the problem. It was caused by lenses. The culprit was me saving my custom lenses to my template. All I had to do to fix it was to open my template and at the top right the box for lenses I chose "none" instead of my custom lenses.
It seems like Plat remembers the very last setting chosen for lenses and automatically loads that lenses after a CWP or CWT opens. After saving this change to my template I went ahead and chose my custom lenses, so now when my template opens, it has my custom lenses selected not “none”.
Apparently since I was saving the lenses setting in my template I was getting a double selection for my custom lenses and Splat I assume looked at that as a change to the file and prompted "save changes". Well that's my theory, maybe someone with more knowledge has a better one. But regardless I don't have that errant prompt anymore
In my case since I’m not currently using different lenses just my own custom one, I’m not bothered by this. Maybe one day when I am using a different lenses for mixing, I may not like this limitation when starting a new project, so I still think it’s a bug and will report it.